CHICAGO (CBS) — A top political reporter at the Chicago Sun-Times resigned on Wednesday, and pointedly accused Bruce Rauner’s campaign aides of intimidation and interference with his reporting and called into question the newspaper’s independence.

“Today, I’m faced with a difficult decision due to the disturbing developments I’ve experienced in the last two weeks that cannot be reconciled with this newspaper’s storied commitment to journalism,” Dave McKinney, who was the Springfield bureau chief at the paper for about 20 years, wrote in a letter to the paper’s boss, Michael Ferro.

Earlier this month, McKinney, along with NBC 5’s Carol Marin, wrote a story that detailed “hard-ball tactics” by Rauner in his dealings with one of his companies, LeapSource.

According to the story, the lawsuit alleged that Rauner told Kirk in February 2001: “If you go legal on us, we’ll hurt you and your family.”

As he worked on the story, McKinney said, the Rauner campaign “used multiple tactics to block it, including having campaign staffers vowing to “go over” our heads. We are accustomed to such tactics.”

But the campaign went a step further, McKinney said.

“But what does not come with the territory is a campaign sending to my boss an opposition-research hit piece–rife with errors–about my wife, Ann Liston. The campaign falsely claimed she was working with a PAC to defeat Rauner and demanded a disclaimer be attached to our story that would have been untrue. It was a last-ditch act of intimidation.”

McKinney’s wife does political consulting work for Democrats. Before the couple married, they hammered out a binding agreement–a “firewall”–that said Liston would not work on, or profit from, the Illinois governor’s race.

In a statement, Rauner campaign spokesman Lance Trover said “publishing the story was irresponsible” because the lawsuit was “tossed out in court and sworn depositions contradict the allegations.”

Trover also accused McKinney of “an extraordinary conflict of interest – married to a Democrat operative with deep connections to an attack group that has spent millions attacking Bruce Rauner.”

Trover added that “no one reached out to Mr. Ferro” about McKinney’s work.

What happened to McKinney next gets murkier and raises serious questions about the integrity of the paper.

Several days after the story was published, McKinney was inexplicably placed on leave–removing a veteran political reporter from covering one of the hottest races in the nation less than a month before Election Day.

The Sun-Times editor, Jim Kirk, allowed McKinney back on the beat after about a week, after finding Rauner’s questions about McKinney’s work totally unfounded.

However, the bizarre behavior at the Sun-Times continued, McKinney said.

“On the first day back, I was advised I shouldn’t have a byline on a LeapSource-related story “right out of the gate” even though it was a legitimate follow-up to our initial story. While later relenting and offering me a contributing byline after I protested, the newspaper had failed an important test: It was not permitting me to do my job the way I had been doing it for almost two decades.

“Was all this retaliation for breaking an important news story that had the blessing of the paper’s editor and publisher, the company’s lawyer and our NBC5 partners?

“Does part of the answer lie in what [Jim] Kirk told me – that you [Ferro] couldn’t understand why the LeapSource story was even in the paper?

Raising even more suspicion about the paper’s independence, the Sun-Times reversed its ban on political endorsements and threw its support behind Rauner.

“Readers of the Sun-Times need to be able to trust the paper. They need to know a wall exists between owners and the newsroom to preserve the integrity of what is published. A breach in that wall exists at the Sun-Times.

“It’s had a chilling effect in the newsroom. While I don’t speak for my colleagues, I’m aware that many share my concern. I’m convinced this newspaper no longer has the backs of reporters like me.”

Jim Kirk emailed the following statement on Wednesday afternoon:

“It is with reluctance that I accept Dave McKinney’s resignation. As recently as this Monday on our Op/Ed page, I stated that Dave is among the best in our profession. I meant it then and I mean it now. The pause we took last week was to ensure there were no conflicts of interest and was taken simply to protect Dave McKinney, the Sun Times and its readers as we were under attack in a heated political campaign. We came to the right result, found the political attacks against us to be false and we stand by our reporting, our journalists and this great newspaper.

“I disagree with Dave’s questioning the integrity of this newspaper and my role as editor and publisher. I call the shots. While I’ve been here, our ownership and management have never quashed a story and they have always respected the journalistic integrity of this paper.”

Disclosure Note:John Dodge worked at the Chicago Sun-Times from 1993-2003